[gmx-developers] trjconv defaults

[David van der Spoel]

David Mobley wrote:
> That's a good idea. Anything to make this more transparent would help, I think.
> 
> David
> 
> 
> On Fri, Oct 17, 2008 at 10:37 AM, Berk Hess <hessb at mpip-mainz.mpg.de> wrote:
>> We could implement a proper solution for this.
>>
>> An option one would be:
>> -pbc nojump
>> center on protein
>> -pbc mol
>> But then all in one call of trjconv
>>

We should probably implement something where we  do operations on 
trajectories in the order of the command line. All the operations then 
have to go into subroutines and we would introduce a loop over the 
options. In that manner the main loop becomes much simpler, and one 
could do anything that trjconv can do in go instead of calling it many 
times. It would be much faster as well.



>> Berk
>>
>>
>> David Osguthorpe wrote:
>>>> I can't even count how many times there are e-mails on the users list
>>>> where people complain that their ligand doesn't stay bound to the
>>>> protein; usually it's pbc problems. (Perhaps it's a good idea to
>>>> actually put a suggestion relating to this in the documentation?)
>>>>
>>>>
>>> Id also like to second this - the right magic trick to get ligands
>>> to be in their binding site is somtimes quite complicated
>>> - cluster has worked for me but also gets into an infinite loop sometimes
>>> - Im still running 3.3.1 to maintain numerical consistency - ie.
>>> I can reproduce trajectories at the binary level
>>>
>>> David
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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